Variant report

Variant	rs954730
Chromosome Location	chr14:64330196-64330197
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr14:64330007-64330205	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr14:64330113-64330450	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64319483..64322302-chr14:64328481..64332813,5	MCF-7	breast:
2	chr14:64319166..64320923-chr14:64328806..64331982,4	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11158508	0.81[ASN][1000 genomes]
rs11158510	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11158512	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11158516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11845009	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11845533	0.80[ASN][1000 genomes]
rs11847056	0.85[ASN][1000 genomes]
rs11848677	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11850357	0.85[ASN][1000 genomes]
rs12147063	0.84[ASN][1000 genomes]
rs12586475	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12587472	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12588087	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12589129	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12589296	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12878017	0.86[ASN][1000 genomes]
rs12880638	0.83[ASN][1000 genomes]
rs12883973	0.81[ASN][1000 genomes]
rs12886839	0.85[ASN][1000 genomes]
rs12890491	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12892314	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12894053	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12894864	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1959034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1959035	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2007726	0.84[ASN][1000 genomes]
rs2149677	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2150291	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2210650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2275018	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2356996	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2357002	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2357003	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34780876	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243627	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4480718	0.81[ASN][1000 genomes]
rs4591051	0.84[ASN][1000 genomes]
rs4899118	0.82[ASN][1000 genomes]
rs4902247	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902248	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573534	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573535	0.84[YRI][hapmap]
rs7143343	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7143535	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7145302	0.90[YRI][hapmap]
rs7145657	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7146821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7148088	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7148584	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7149766	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7153101	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7154239	0.81[ASN][1000 genomes]
rs7155129	0.85[ASN][1000 genomes]
rs7157314	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7157323	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7158974	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7160127	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7493416	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7493843	0.85[ASN][1000 genomes]
rs8005553	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8005831	0.81[ASN][1000 genomes]
rs8005899	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8008552	0.85[ASN][1000 genomes]
rs8015158	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8015311	0.85[ASN][1000 genomes]
rs8015354	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8022917	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs945030	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs951250	0.82[YRI][hapmap]
rs9707224	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs998241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64321200-64333800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:64321200-64334600	Weak transcription	Pancreas	Pancrea
3	chr14:64321200-64340600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:64321400-64330600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr14:64321400-64331200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:64321400-64350200	Weak transcription	Fetal Stomach	stomach
7	chr14:64322400-64334400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr14:64322600-64331200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:64322600-64331200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr14:64322800-64330600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr14:64322800-64330800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr14:64322800-64340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:64322800-64340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:64323000-64330200	Weak transcription	Primary T cells from cord blood	blood
15	chr14:64323000-64330400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr14:64323000-64332800	Weak transcription	Fetal Intestine Small	intestine
17	chr14:64323000-64333000	Weak transcription	Ovary	ovary
18	chr14:64323200-64331200	Weak transcription	Right Atrium	heart
19	chr14:64323200-64334400	Weak transcription	Aorta	Aorta
20	chr14:64323200-64340200	Weak transcription	Left Ventricle	heart
21	chr14:64323200-64340400	Weak transcription	Spleen	Spleen
22	chr14:64324000-64330200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr14:64324200-64330800	Weak transcription	Hela-S3	cervix
24	chr14:64324400-64330800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr14:64324400-64331200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr14:64324600-64331000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr14:64324600-64331200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr14:64324600-64341400	Weak transcription	HSMM	muscle
29	chr14:64325800-64331000	Enhancers	Placenta	Placenta
30	chr14:64326600-64330800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr14:64326800-64331600	Enhancers	Stomach Mucosa	stomach
32	chr14:64327000-64330600	Enhancers	Dnd41	blood
33	chr14:64327000-64331400	Weak transcription	Thymus	Thymus
34	chr14:64327200-64331200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr14:64327200-64332000	Weak transcription	Fetal Brain Female	brain
36	chr14:64327200-64340600	Weak transcription	Right Ventricle	heart
37	chr14:64327400-64330800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr14:64327400-64330800	Weak transcription	Fetal Intestine Large	intestine
39	chr14:64327400-64331000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr14:64327400-64331000	Weak transcription	Fetal Heart	heart
41	chr14:64327400-64333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr14:64327600-64360000	Weak transcription	Gastric	stomach
44	chr14:64327800-64334400	Weak transcription	Lung	lung
45	chr14:64327800-64342200	Weak transcription	Esophagus	oesophagus
46	chr14:64328400-64330600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr14:64328400-64335000	Weak transcription	Psoas Muscle	Psoas
48	chr14:64328600-64331400	Flanking Active TSS	GM12878-XiMat	blood
49	chr14:64328800-64330400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr14:64329000-64330800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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